Different Types of DNA Conformations

DNA, the genetic information carrier molecule of the cell, is a long polymer of nucleotides and can adopt different types of structural conformations. The various types of conformations that the DNA can adopt depend on different factors such as:

1.      Hydration level
2.      Salt concentration
3.      DNA sequence
4.      Quantity and direction of super-coiling
5.      Presence of chemically modified bases
6.      Different types of metal ions and its concentrations
7.      Presence of polyamines in solution.

The most common types of structural conformations of DNA are named as:

(1).  A-DNA
(2).  B-DNA
(3).  Z-DNA

Among these three types, the most abundant type of DNA is B-DNA, commonly known as Watson-Crick Model of DNA double helix. The present post describes the structural features of A, B and Z forms of DNA in a comparative manner. We will also discuss the similarities and differences between A-DNA, B-DNA and Z-DNA.

(1). A-DNA

A-DNA is a rare type of structural conformation that a DNA can adopt under dehydrating conditions. A-DNA is a double stranded helical structure almost similar to B-DNA but with a shorter and more compact structural organization. A-DNA was discovered by Rosalind Franklin and the credit for the naming of A-DNA and B-DNA was also accounted to her. Important structural features of A-DNA are given below:

Ø  A-DNA is formed from B-DNA under dehydrating condition.
Ø  A-DNA is much wider and flatter than B-DNA.
Ø  Similar to B-DNA, the A-DNA is also a right handed helix.
Ø  The helix diameter of A-DNA is 26 Å.

(image source: cc wikipedia)

Ø  The helix pitch (height of a turn) of A-DNA is 28.6 Å.
Ø  A DNA is 20 to 25% shorter than B-DNA due to the smaller rise per turn.
Ø  A-DNA contains 11.6 base pairs per turn.
Ø  The distance between the adjacent base pairs is 2.9 Å.
Ø  The helical twist per base pair in A-DNA is 31⁰.
Ø  A-DNA has an axial hole at the centre (hollow central core).

Ø  In A-DNA the base pairs are inclined to the helical axis.

Ø  Individual base pairs in A-DNA are 20⁰ tilted with respect to the helical axis.

Ø  A-DNA has narrow and deep major groves.

Ø  The minor groves of A-DNA are wide and shallow.

Ø  The deoxyribose sugar pucker in A-DNA is C3’endo form

Ø  The conformation of gycosidic bond in A-DNA is in Anti- form.

(2). B-DNA

The B-DNA is the most common and predominate type of structural conformation of DNA in the cells. The DNA prefers to occur in B form under the natural physiological conditions (pH and salt concentration) in the cell. The B-DNA is better described as the Watson – Crick Model of DNA described for the first time by James Watson and Francis Crick. Important structural features of B-DNA are given below:

Ø  Majority of the DNA in a cell is in B-DNA conformation.
Ø  B-DNA is a right handed helix.
Ø  In B-DNA, the bases occupy at the core whereas the sugar phosphate backbone occurs at the peripheral portion of the helix.
Ø  In B-DNA only the edges of the base pairs are exposed to the solvent.
Ø  Each base pair in B-DNA has the same width.
Ø  The width of A – T and G – C in B-DNA is 10.85 Å.

Ø  The helical diameter of B-DNA is 20 Å.

Ø  Each turn on helix in B-DNA possess a helical height of 34 Å.

Ø  Each turn in the B-DNA consists of 10 base pairs.

Ø  The distance between adjacent base pairs in B-DNA is 3.4 Å.

Ø  Each base pair will have a helical twist of 36⁰ (360/10).

Ø  The plain of inter-strand hydrogen bonds are perpendicular to the helical axis.

Ø  B-DNA has a solid central core.

Ø  The major grove of B-DNA is wide and deep.

Ø  The minor grove of B-DNA is narrow and deep.

Ø  The sugar pucker in B-DNA is C2’ endo form.

Ø  The glycosidic bond conformation in B-DNA is in anti- form.

(3). Z-DNA

Z-DNA is a left-handed double helical conformation of DNA in which the double helix winds to the left in a zig-zag pattern. The DNA strand with complementary nucleotides with alternating purines and pyrimidines (such as poly-d(GC).poly-d(GC) or poly-d(AC).poly-d(GT)) can form Z DNA conformation at high salt concentration. The existence of Z DNA was discovered by Andres Wang and Alexander Rich. Z-DNA is one of the biologically active forms of DNA found in vivo in the cells. The exact biological function of Z-DNA is not clear. The Z-DNA is usually located upstream of the start site of a gene and thus it may have some role in the regulation of gene expression. Important structural features of B-DNA are given below:

Ø  The Z-DNA is a left handed helical structure.
Ø  The double helix winds in a zig-zag pattern.
Ø  The helical diameter of Z-DNA is 18 Å.
Ø  The total height of a helix turn is 44 Å.
Ø  The nucleotide pairs in Z-DNA occur as nucleotide dimers.

Ø  Each helical turn of Z-DNA contains 12 nucleotides (6 dimers).

Ø  The helical turn per base pair in Z-DNA is 9⁰ for pyrimidine – purine step and 51⁰ for purine – pyrimidine step.

Ø  The distance between each nucleotide is 7.4 Å.

Ø  Z-DNA possesses a more or less flat major grove.

Ø  The minor grove in Z-DNA is narrow and deep.

Ø  Z-DNA has a solid core at the centre.

Ø  The sugar pucker is C2’ endo for pyrimidine and C3’endo for purines.

Ø  The glycosidic bond conformation is anti- for pyrimidines and syn- for purines.

A comparison table of the structural features of A-DNA, B-DNA and Z-DNA

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